After foiling an attempted train robbery of a valuable treasure, Virginia joins forces with three other Drifters as they travel the world and unravel a mysterious plot involving the ancient history of the planet.

In order to discover new towns and dungeons, the player must ask for information or learn of them during the plot and then manually search for them using a GPS-like system.

Four Drifters find themselves chosen to wield the power of the planet's spiritual protectors, the Guardians, to stop a prophesied but unknown menace to their world.

As they adventure together, they are opposed by other Drifter teams, a trio of fanatical scientists called the Prophets, and the Demons of Filgaian legend.

The other Drifter team is composed of Maya Schrödinger, her brother Alfred, their stylish afro-ed bodyguard, Todd Dukakis, and a mysterious cat named Shady.

Maya has a unique ability among Filgaians to absorb information from books and to use it to improve battle techniques, hence her Calamity Jane persona.

The Prophets are a trio of scientists: Leehalt Alcaste, Melody Vilente, and Malik Bendict, who are obsessed with restoring Filgaia's decaying environment, but they do not care who suffers as a result.

He acquires the three shields collected by Janus earlier, "Andro", "Crio", and "Hieraco", and applies their power to the prophets, making himself three new demon followers, akin to Alhazad, Harken, and Belselk of the first game.

Contrary to the way she apparently shows up out of nowhere, she can be encountered as a random NPC in some of the game's towns, but can't be addressed, as she will be gone if the party reaches where she is.

Beatrice ultimately reveals herself to be playing the role of the great manipulator, as every major event in the game can somehow be attributed to her.

She had used members of the Council of Seven to attempt to sabotage the Yggdrasil, and create her Filgaia, ten years prior, which led to the defoliation of the planet, after which she removed everyone's memory of the event.

The experiment went awry and did the exact opposite, sucking most of the remaining life from the planet, leaving most of it an expansive desert.

Rounding out the group are Jet's adoptive father/creator, Elliot Enduro, as well as Pete Inkapilia, and Duran Bryant, about whom little is revealed, but their notes detail that they were repeatedly visited by Beatrice in dreams.